[2023-03-17 04:15:16,792] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:16,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:16,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference
[2023-03-17 04:15:17,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:17,975] [INFO] Task started: Prodigal
[2023-03-17 04:15:17,975] [INFO] Running command: cat /var/lib/cwl/stgf6bc36ca-f8ad-4db8-bd53-f5e54b8a4c03/OceanDNA-b28235.fa | prodigal -d OceanDNA-b28235/cds.fna -a OceanDNA-b28235/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:32,183] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:32,183] [INFO] Task started: HMMsearch
[2023-03-17 04:15:32,183] [INFO] Running command: hmmsearch --tblout OceanDNA-b28235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/reference_markers.hmm OceanDNA-b28235/protein.faa > /dev/null
[2023-03-17 04:15:32,425] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:32,426] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf6bc36ca-f8ad-4db8-bd53-f5e54b8a4c03/OceanDNA-b28235.fa]
[2023-03-17 04:15:32,446] [INFO] Query marker FASTA was written to OceanDNA-b28235/markers.fasta
[2023-03-17 04:15:32,447] [INFO] Task started: Blastn
[2023-03-17 04:15:32,447] [INFO] Running command: blastn -query OceanDNA-b28235/markers.fasta -db /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/reference_markers.fasta -out OceanDNA-b28235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:33,001] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:33,002] [INFO] Selected 17 target genomes.
[2023-03-17 04:15:33,002] [INFO] Target genome list was writen to OceanDNA-b28235/target_genomes.txt
[2023-03-17 04:15:33,011] [INFO] Task started: fastANI
[2023-03-17 04:15:33,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6bc36ca-f8ad-4db8-bd53-f5e54b8a4c03/OceanDNA-b28235.fa --refList OceanDNA-b28235/target_genomes.txt --output OceanDNA-b28235/fastani_result.tsv --threads 1
[2023-03-17 04:15:43,993] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:43,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:43,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:44,003] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:44,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:44,003] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	83.275	561	709	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	83.2396	562	709	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	78.1654	248	709	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	78.1207	208	709	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	78.113	252	709	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	78.0859	258	709	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.0606	234	709	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.9929	233	709	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.9929	233	709	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	77.6418	228	709	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.4231	150	709	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	77.4204	152	709	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.3881	204	709	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.4416	90	709	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.1357	124	709	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.888	78	709	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.888	78	709	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:44,003] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28235/tc_result.tsv
[2023-03-17 04:15:44,004] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:44,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:44,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/checkm_data
[2023-03-17 04:15:44,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:44,009] [INFO] Task started: CheckM
[2023-03-17 04:15:44,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28235/checkm_input OceanDNA-b28235/checkm_result
[2023-03-17 04:16:22,845] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:22,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:22,848] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:22,848] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:22,848] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28235/markers.fasta)
[2023-03-17 04:16:22,849] [INFO] Task started: Blastn
[2023-03-17 04:16:22,849] [INFO] Running command: blastn -query OceanDNA-b28235/markers.fasta -db /var/lib/cwl/stg282eca0b-c913-4957-8ec8-6b86d396a7e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:23,425] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:23,426] [INFO] Selected 15 target genomes.
[2023-03-17 04:16:23,426] [INFO] Target genome list was writen to OceanDNA-b28235/target_genomes_gtdb.txt
[2023-03-17 04:16:23,497] [INFO] Task started: fastANI
[2023-03-17 04:16:23,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6bc36ca-f8ad-4db8-bd53-f5e54b8a4c03/OceanDNA-b28235.fa --refList OceanDNA-b28235/target_genomes_gtdb.txt --output OceanDNA-b28235/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:33,726] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:33,735] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:33,735] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_004566265.1	s__Epibacterium sp004566265	98.1573	379	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	98.66	98.66	0.83	0.83	2	conclusive
GCF_001458415.1	s__Epibacterium multivorans	83.2754	561	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001681715.1	s__Epibacterium mobile	78.1654	248	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_009496005.1	s__Epibacterium litoralis	78.1105	207	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003215.1	s__Epibacterium scottomollicae	78.088	256	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	78.0075	232	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_000813965.1	s__Leisingera sp000813965	77.885	234	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014065.1	s__Epibacterium sp000014065	77.8831	253	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	77.8503	241	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265095.1	s__Epibacterium sp006265095	77.8162	237	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	77.796	212	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617595.1	s__Epibacterium aquimaris	77.6445	226	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458435.1	s__Thalassobius mediterraneus	77.3909	152	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003318255.1	s__Ruegeria sp003318255	76.985	140	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214715.1	s__JABSSB01 sp013214715	76.7161	113	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:33,735] [INFO] GTDB search result was written to OceanDNA-b28235/result_gtdb.tsv
[2023-03-17 04:16:33,735] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:33,737] [INFO] DFAST_QC result json was written to OceanDNA-b28235/dqc_result.json
[2023-03-17 04:16:33,737] [INFO] DFAST_QC completed!
[2023-03-17 04:16:33,737] [INFO] Total running time: 0h1m17s